Several years ago I had a similar problem on my RV7A after I purchased it from the original owner/builder. Both magnetometers were mounted on the deck shelf below the vertical stabilizer. Heading would vary every time I talked on the radio and/or moved my rudder. Chased that dog for several months until a long conversation with the GRT tech rep convinced me to move my magnetometers to the wing tips. Once I did that heading issues disappeared.

Not sure if this is your problem but in your setup configuration there is probably some way to check "counters" to see if there are decreases or increase number count rates to confirm. Just my two cents. Good luck.